BIOL368/S20:Class Journal Week 6

Christina Dominguez's Response

In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).

I learned about HIV and how it can be studied scientifically. HIV is a disease that is very culturally prominent and I feel as though I did not know anything about it from a scientific standpoint. This project helped me to understand it in a scientific aspect which I enjoyed doing. I learned how to use data from a paper to make phylogenetic trees for my technical skills. I never knew that this software existed and I thought it was easy to use and helpful. I learned that getting a head start on the presentation is very helpful at making small edits that make the presentation better. Teamwork helped for us to both be motivated to get it done with the best quality for the time we had.

What is still not clear to you after having concluded this project?

I would have liked to known the statistical test they ran for their slope of diversity and divergence significance. It is not clear how they determined what was significant and not, which made it hard for us to do so.

If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?

I would like to rework this project by switching progressor group categorization into different criteria and looking at how this effects the results. This could challenge any standard way of categorizing HIV patients and potentially find a better way to categorize.

Cdominguez (talk) 12:13, 26 February 2020 (PST)

Annika Dinulos

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • I learned that it's hard to follow methods and replicate parts of a study done from a research journal. While my partner and I were working on our project, we realized that the statistical analysis information was not included in the results or the methods, which made it hard for us to compare our results with the results. However, I also learned to take initiative and analyze the results anyways because the scientific work that I am doing is valid. I learned that HIV is extremely complex and in in the lens of a scientist, hard to categorize and quantify. I learned that I appreciate a partner who puts in equal effort and is willing to meet and discuss throughout the whole process, not just a day before.
2. What is still not clear to you after having concluded this project?
   • It is still not clear how analysis was run, Christina and I struggled with how results were observed, especially since we didn't necessarily find significance. It is still unclear what nonprogressor trees look like, so that would be nice to look at in the future.
3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
   • In the future, I would like to take actual averages and not just median averages but weighted averages that take into account the number of visits and not just observations. I feel like this information would be more quantitative and precise when computing results.

Adinulos (talk) 13:58, 26 February 2020 (PST)

Jack Menzagopian

1. This project was really the first time I understood the vast the scope of the scientific lens can be. By seeing how many ways my peers and I could think of to analyze just one data set really put in perspective for me that science is not as simple as I thought. I also learned how to take multiple useful ways of analyzing data and connect them together to create a well developed and well rounded analysis of data. Before this project, I did not know how readily available some of the tools we used were. I also learned the importance of constant communication with team members.
2. I still don't understand how to best use and present statistical data, both from how the paper used it and how it was used in this project.
3. I would like to look at mutations in the same windows we did but throughout HIV development to see if some windows are favored during specific stages of development after seroconversion, leading to rapid progression and the widespread diversity along the gene that was seen during the last visit.

Jmenzago (talk) 14:39, 26 February 2020 (PST)

Nicholas Yeo

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • Scientifically, I learned that there is a slight correlation between the genetic diversity of HIV-1 viral strains and the CD4 T-cell levels of the subject at hand. I also learned that multiple discoveries can be made from a single study, even if the study was not designed to allow for those discoveries. Technically, I learned how to interpret scatterplots and statistical information in regard to the scientific context. Looking back at the project, I discovered that I value partner proactivity and personality when working in a team, because that is the environment in which I work best.
2. What is still not clear to you after having concluded this project?
   • It is still not clear to me how the progressor groups were made. It seems like the creation of the groups created more noise that clouded understanding of the article.
3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
   • I would like to take the project in more of a treatment-type direction. I believe that the knowledge gathered is useless unless it can be applied in a beneficial way. This firstly would most likely require more significant data, and so I would want to use a bigger group of people with more consistency. Although this is difficult to accomplish, I think that is necessary.

Nyeo2 (talk) 23:23, 26 February 2020 (PST)

Maya Paniagua

In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).

• In addition to learning that rapid and moderate progressors could be categorized in the same group, I learned with my head what theta means in terms of biology, I learned with my hands how to align sequences and from that gather valuable information about diversity and divergence, and I learned with my heart as a scientist it is important to constantly be open to new ideas.

What is still not clear to you after having concluded this project?

• It is still not clear to me how the authors decided which group each subject belonged to if there was no significant difference between the groupings.

If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?

• If I had more time to continue this project I would develop this project with more subjects, who were more consistent with their visits in an effort to get a significant difference between the rapid and moderate progressors.

Mpaniag1 (talk) 15:59, 26 February 2020 (PST)

Karina Vescio

• In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
  • I learned that doing scientific research can be quite tedious and difficult when there is not enough data, or there is data that inconclusive. I also learned that a lot of research is bias, considering they are performed and written about by people. I learned how to use bioinformatics to look at gene sequencing, create phylogenic trees. I learned how to study the relationship between phylogenetic trees and mutation of viruses. I also learned that it is important to have all scientists involved in the research, dedicated to the findings.
• What is still not clear to you after having concluded this project?
  • To me it is unclear as to why the HIV virus mutated much more rapidly in some subjects verses others. I wish the scientists in the original research would have had some sort of explanation, or discussed whether some patients were experimenting with different treatments, or how they took care of themselves.
• If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
  • I would like to look further into the immune system factors associated with the HIV virus. I would also like to study individuals who are immune to the virus, and hopefully learn more about why that is, and if there can be a way to use their DNA in order to help those who have the virus.

Kvescio (talk) 22:19, 26 February 2020 (PST)

Drew Cartmel

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • In terms of scientific knowledge, I learned that conclusions made by authors of scientific papers can be utilized in many different ways by other researchers to further contribute to the scientific communities' knowledge on a particular concept. I terms of technical skills, from this project I learned that many of the tools that researchers use to conduct their experiments are available to the public and all that is needed is proper instruction on how to properly utilize these tools. In terms of teamwork qualities needed to succeed as a scientist, I learned that it is helpful to have partners that are reliable and also are willing to build off of each others ideas to create more encompassing research results.
2. What is still not clear to you after having concluded this project?
   • What is still not clear after concluding this project is how statistical analyses were used to back up the results that were found in this paper.
3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you take for this project?
   • If I had more time, a possible future direction that I could take for this project would be to compare the sequences of all of the subjects at each visit that fell under the category of the rapid progressors and see if their genetic sequences have any defining factors that could be used to recognize rapid progressing HIV individuals in the future.

Dcartmel (talk) 19:56, 26 February 2020 (PST)

Madeleine King

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   • In addition to the scientific conclusion, I learned how to data cleanse someone else’s study in order to contribute to knowledge of the evolution of the HIV-1 virus. I also learned more about the HIV-1 virus, and how much of a problem it is for the medical community due to the high mutation rate. On the other hand, I also debunked some common myths about HIV-1 and gained a better understanding of HIV-1 and how it affects developing and wealthy communities alike. Lastly, I learned how to work together with a partner on a project by splitting up work as well as working together outside of class for feedback, clarity, and practice.
2. What is still not clear to you after having concluded this project?
   • What is still not clear to me after concluding this project is why they classified rapid and moderate progressors into different groups. I can understand why but they did not say their reasoning behind it besides the CD4 cell count numbers.
3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
   • I’d like to conduct this study with a bigger cohort size (if possible), and more consistent visits in order to get more uniform data. I’d also think it would be interesting to take subjects from around the world and compare them to see if the viruses are different in anyway.

Mking44 (talk) 20:15, 26 February 2020 (PST)

Nathan On

In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).

• I learned more about the process of performing new research and trying to find the best way to analyze data. When using Excel, I learned that you have to be precise and formulaic to ensure that any formulas and equations are applied correctly, otherwise you risk messing up your data. It took a lot of perseverance to stare at a number filled screen for hours trying to find out what you messed up in a long equation.

What is still not clear to you after having concluded this project?

• Some of the statistics used by the Markham paper still confuse me. When we were trying to decide which stats to try to integrate into our project, we had trouble deciphering their meaning.

If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?

• I would like to study the amino acid sequences and/or protein structures to see more specifically the effects on the env protein and HIV virulence

Non (talk) 23:36, 26 February 2020 (PST)

Carolyn Egekeze

1. In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
   1. In doing this project, I learned that despite all of the studies looking at HIV's gp120 region, there is still so much that we don't know that could be useful for developing a vaccine. For example, studying the evolutionary patterns of the virus and looking closely at where the sequences are changing the most can help us to figure out how the infection progresses.
2. What is still not clear to you after having concluded this project?
   1. One thing that still is not clear is how the sequence changes at the hotspots might affect how quickly the virus progresses. In addition, I am still interested in learning why clones from the subjects in the same progressor groups did not share close evolutionary relationships to each other.
3. If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
   1. If I had more time, I want to see if looking at the amino acid sequence that is produced from the gene sequence shows a similar degree of changes between the progressor groups. In addition, I think that looking at a different region of the HIV genome and having a study that includes more people can help with determining how HIV-1 evolves and what regions could serve as good clinical targets. Finally, I would want to determine if the immune system of the patient plays an active role in determining how quickly the virus progresses.

Carolyne (talk) 22:31, 26 February 2020 (PST)

Jenny Chua

In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).

I learned the implications theta had on CD4 T-cell values and how to interpet that data graphically with my head, I learned how to statistically analyze y- and x-values on a linear regression with my hands, and I learned how usable one set of data can be, as it was analyzed several different ways between my fellow BIOL368 classmates.

What is still not clear to you after having concluded this project?

I still don't know why theta values weren't recorded at every visit for every subject, and I also don't know exactly why non-progressor or moderate progressor data revealed a direct relationship.

If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?

I would love to try to re-create this project, but have the same number of patients, visits, and theta values. While theta doesn't necessarily take into account the amount of visits, I think it would make our regression and correlation results stronger in the end.

Jennymchua (talk) 22:33, 26 February 2020 (PST)

Lizzy Urbina

• In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
  • From a scientific point of view I learned about the complexity of HIV and the different ways in can develop in a person, additionally, the behavior it has can vary person to person. Technically, I feel more coffident using DNA analysis tools, I undertand phlylogenetic trees better, moreover I gained more practice using some excel tools. Teamwork qualities, I learned to be patient and appreciate people's time and the imporatance of being fully present when working in a project.

• What is still not clear to you after having concluded this project?
  • I am still curous to know why nonprogressor tend to favor absence of change and lack of diversity when evolution favors diversity. Addtionally, I am curious of other factors that could have influence these data.

• If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
  • I would like to study the immune system respose in the different classification of subject, the way antibodies respond to the infection and interaction of the recpetors. Addtionally, I would consider outside factors that could affect the data and look for correlation among them.

Lurbinah (talk) 23:53, 26 February 2020 (PST)

Sahil Patel

• In addition to the scientific conclusion for your project, reflect on what you learned as a person by performing this research. Describe what you learned with your head (scientific knowledge), hands (technical skills), and heart (personal or teamwork qualities needed to succeed as a scientist).
  • I learned about how one's own biases can often reflect in the work that is put out there. Especially if research was done as a team, depending on who is charge of what, certain data can be represented in a way that can support the conclusion that the person is trying to reach. This paper was published in 1998, yet we are still so far from uncovering all there is to now about HIV. But with the new skills I have learned, I as well as others like me will help the scientific community in its pursuit of new information.
• What is still not clear to you after having concluded this project?
  • It is still not clear to me how one can know if they are doing research or answering questions that have already been asked. Is google or other search engines our only hope in exploring this?
• If you had more time (anywhere from a few more weeks to a couple of years, like, for example, a Master's thesis project), what future directions would you like to take for this project?
  • I would love to see this project head into a direction that is goal-oriented. I feel like it is so easy to get lost in the little things because this is such a nuanced subject but it is important to look at the big picture. For HIV research, it is finding a universal vaccine. If scientists in the past believed that we were so close, why does it feel that as we uncover new information, we are simply finding ourselves in as deeper hole?

Sahil Patel (talk) 00:02, 27 February 2020 (PST)